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          <a class="navbar" target="_top" href="http://code.google.com/p/weblogo/">WebLogo</a>
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        Package&nbsp;weblogolib
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<!-- =========== START OF PACKAGE DESCRIPTION =========== -->
<h2 class="package">Package weblogolib</h2>

<pre class="literalblock">
WebLogo (http://code.google.com/p/weblogo/) is a tool for creating sequence 
logos from biological sequence alignments.  It can be run on the command line,
as a standalone webserver, as a CGI webapp, or as a python library.

The main WebLogo webserver is located at http://bespoke.lbl.gov/weblogo/

Please consult the manual for installation instructions and more information:
(Also located in the weblogolib/htdocs subdirectory.)

    http://bespoke.lbl.gov/weblogo/manual.html

For help on the command line interface run
    ./weblogo --help

To build a simple logo run
    ./weblogo  &lt; cap.fa &gt; logo0.eps
    
To run as a standalone webserver at localhost:8080 
    ./weblogo --server

To create a logo in python code:
    &gt;&gt;&gt; from weblogolib import *
    &gt;&gt;&gt; fin = open('cap.fa')
    &gt;&gt;&gt; seqs = read_seq_data(fin) 
    &gt;&gt;&gt; data = LogoData.from_seqs(seqs)
    &gt;&gt;&gt; options = LogoOptions()
    &gt;&gt;&gt; options.title = &quot;A Logo Title&quot;
    &gt;&gt;&gt; format = LogoFormat(data, options)
    &gt;&gt;&gt; fout = open('cap.eps', 'w') 
    &gt;&gt;&gt; eps_formatter( data, format, fout)


-- Distribution and Modification --
This package is distributed under the new BSD Open Source License. 
Please see the LICENSE.txt file for details on copyright and licensing.
The WebLogo source code can be downloaded from http://code.google.com/p/weblogo/
WebLogo requires Python 2.3, 2.4 or 2.5, the corebio python toolkit for computational biology (http://code.google.com/p/corebio), and the python array 
package 'numpy' (http://www.scipy.org/Download)
</pre>
<hr/>

<!-- =========== START OF SUBMODULES =========== -->
<table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="details">
  <th colspan="2">Submodules</th></tr>
  <tr><td><ul>
<li> <b><a href="weblogolib.color-module.html"><code>color</code></a></b>: <i>Color specifications using CSS2 (Cascading Style Sheet) syntax.</i>
<li> <b><a href="weblogolib.colorscheme-module.html"><code>colorscheme</code></a></b>: <i>Popular color codings for nucleic and amino acids.</i>
  </ul></td></tr>
</table><br />


<!-- =========== START OF CLASSES =========== -->
<table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="summary">
  <th colspan="2">Classes</th></tr>
<tr><td width="15%">
  <b><a href="weblogolib.Dirichlet-class.html"><code>Dirichlet</code></a></b></td>
  <td>The Dirichlet probability distribution.</td></tr>
<tr><td width="15%">
  <b><a href="weblogolib.GhostscriptAPI-class.html"><code>GhostscriptAPI</code></a></b></td>
  <td>Interface to the command line program Ghostscript ('gs')...</td></tr>
<tr><td width="15%">
  <b><a href="weblogolib.LogoData-class.html"><code>LogoData</code></a></b></td>
  <td>The data needed to generate a sequence logo.</td></tr>
<tr><td width="15%">
  <b><a href="weblogolib.LogoFormat-class.html"><code>LogoFormat</code></a></b></td>
  <td>Specifies the format of the logo.</td></tr>
<tr><td width="15%">
  <b><a href="weblogolib.LogoOptions-class.html"><code>LogoOptions</code></a></b></td>
  <td>A container for all logo formating options.</td></tr>
<tr><td width="15%">
  <b><a href="weblogolib.LogoSize-class.html"><code>LogoSize</code></a></b></td>
  <td>&nbsp;</td></tr>
</table><br />


<!-- =========== START OF FUNCTION SUMMARY =========== -->
<table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="summary">
  <th colspan="2">Function Summary</th></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><a name="base_distribution"></a><span class="summary-sig"><span class="summary-sig-name">base_distribution</span>(<span class=summary-sig-arg>percentCG</span>)</span></code>
</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#eps_formatter" class="summary-sig-name"><code>default_formatter</code></a>(<span class=summary-sig-arg>logodata</span>,
          <span class=summary-sig-arg>format</span>,
          <span class=summary-sig-arg>fout</span>)</span></code>
<br />
Generate a logo in Encapsulated Postscript (EPS)...</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#eps_formatter" class="summary-sig-name"><code>eps_formatter</code></a>(<span class=summary-sig-arg>logodata</span>,
          <span class=summary-sig-arg>format</span>,
          <span class=summary-sig-arg>fout</span>)</span></code>
<br />
Generate a logo in Encapsulated Postscript (EPS)...</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><a name="equiprobable_distribution"></a><span class="summary-sig"><span class="summary-sig-name">equiprobable_distribution</span>(<span class=summary-sig-arg>length</span>)</span></code>
</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#jpeg_formatter" class="summary-sig-name"><code>jpeg_formatter</code></a>(<span class=summary-sig-arg>data</span>,
          <span class=summary-sig-arg>format</span>,
          <span class=summary-sig-arg>fout</span>)</span></code>
<br />
Generate a logo in JPEG format.</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#pdf_formatter" class="summary-sig-name"><code>pdf_formatter</code></a>(<span class=summary-sig-arg>data</span>,
          <span class=summary-sig-arg>format</span>,
          <span class=summary-sig-arg>fout</span>)</span></code>
<br />
Generate a logo in PDF format.</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#png_formatter" class="summary-sig-name"><code>png_formatter</code></a>(<span class=summary-sig-arg>data</span>,
          <span class=summary-sig-arg>format</span>,
          <span class=summary-sig-arg>fout</span>)</span></code>
<br />
Generate a logo in PNG format.</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#png_print_formatter" class="summary-sig-name"><code>png_print_formatter</code></a>(<span class=summary-sig-arg>data</span>,
          <span class=summary-sig-arg>format</span>,
          <span class=summary-sig-arg>fout</span>)</span></code>
<br />
Generate a logo in PNG format with print quality (600 DPI) resolution.</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><a name="read_seq_data"></a><span class="summary-sig"><span class="summary-sig-name">read_seq_data</span>(<span class=summary-sig-arg>fin</span>,
          <span class=summary-sig-arg>input_parser</span>,
          <span class=summary-sig-arg>alphabet</span>,
          <span class=summary-sig-arg>ignore_lower_case</span>,
          <span class=summary-sig-arg>max_file_size</span>)</span></code>
</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#txt_formatter" class="summary-sig-name"><code>txt_formatter</code></a>(<span class=summary-sig-arg>logodata</span>,
          <span class=summary-sig-arg>format</span>,
          <span class=summary-sig-arg>fout</span>)</span></code>
<br />
Create a text representation of the logo data.</td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1">&nbsp;</font></td>
  <td><code><span class="summary-sig"><a href="weblogolib-module.html#which_alphabet" class="summary-sig-name"><code>which_alphabet</code></a>(<span class=summary-sig-arg>seqs</span>)</span></code>
<br />
Returns the most appropriate unambiguous protien, rna or dna alphabet
for a Seq or SeqList.</td></tr>
</table><br />


<!-- =========== START OF VARIABLE SUMMARY =========== -->
<table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="summary">
  <th colspan="2">Variable Summary</th></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>str</code></font></td>
<td><b><a href="weblogolib-module.html#__version__"><code>__version__</code></a></b> = <span title="'3.0b12'"><code><span class="variable-quote">'</span>3.0b12<span class="variable-quote">'</span>                                   </code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>ColorScheme</code></font></td>
<td><b><a href="weblogolib-module.html#classic"><code>classic</code></a></b> = <span title="&lt;weblogolib.colorscheme.ColorScheme object at 0x138f790&gt;"><code>&lt;weblogolib.colorscheme.ColorScheme&nbsp;object&nbsp;at&nbsp;<span class="variable-ellipsis">...</span></code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>dict</code></font></td>
<td><b><a href="weblogolib-module.html#default_color_schemes"><code>default_color_schemes</code></a></b> = <span title="{Alphabet( 'ACDEFGHIKLMNPQRSTVWY', zip('acdefghiklmnpqrstvwy', 'ACDEFGHIKLMNPQRSTVWY') ): &lt;weblogolib.colorscheme.ColorScheme object at 0x1356450&gt;, Alphabet( 'ACGU', zip('acgu', 'ACGU') ): &lt;weblogolib.colorscheme.ColorScheme object at 0x13563d0&gt;, Alphabet( 'ACGT', zip('acgt', 'ACGT') ): &lt;weblogolib.colorscheme.ColorScheme object at 0x13563d0&gt;}"><code>{Alphabet(&nbsp;'ACDEFGHIKLMNPQRSTVWY<span class="variable-ellipsis">...</span></code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>str</code></font></td>
<td><b><a href="weblogolib-module.html#description"><code>description</code></a></b> = <span title="'Create sequence logos from biological sequence alignments.'"><code><span class="variable-quote">'</span>Create&nbsp;sequence&nbsp;logos&nbsp;from&nbsp;biological&nbsp;seq<span class="variable-ellipsis">...</span></code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>dict</code></font></td>
<td><b><a href="weblogolib-module.html#formatters"><code>formatters</code></a></b> = <span title="{'eps': &lt;function eps_formatter at 0x1391c30&gt;, 'jpeg': &lt;function jpeg_formatter at 0x1391b30&gt;, 'pdf': &lt;function pdf_formatter at 0x13919f0&gt;, 'txt': &lt;function txt_formatter at 0x1391bf0&gt;, 'png_print': &lt;function png_print_formatter at 0x1391bb0&gt;, 'png': &lt;function png_formatter at 0x1391b70&gt;}"><code>{'eps':&nbsp;&lt;function&nbsp;eps_formatter&nbsp;at&nbsp;0x1391c3<span class="variable-ellipsis">...</span></code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>dict</code></font></td>
<td><b><a href="weblogolib-module.html#std_alphabets"><code>std_alphabets</code></a></b> = <span title="{'protein': Alphabet( 'ACDEFGHIKLMNPQRSTVWY', zip('acdefghiklmnpqrstvwy', 'ACDEFGHIKLMNPQRSTVWY') ), 'dna': Alphabet( 'ACGT', zip('acgt', 'ACGT') ), 'rna': Alphabet( 'ACGU', zip('acgu', 'ACGU') )}"><code>{'protein':&nbsp;Alphabet(&nbsp;'ACDEFGHIKLMNPQRST<span class="variable-ellipsis">...</span></code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>dict</code></font></td>
<td><b><a href="weblogolib-module.html#std_percentCG"><code>std_percentCG</code></a></b> = <span title="{'E. coli': 50.5, 'D. melanogaster': 43.0, 'T. thermophilus': 69.400000000000006, 'H. sapiens': 40.0, 'C. elegans': 36.0, 'S. cerevisiae': 38.0, 'M. musculus': 42.0}"><code>{'E.&nbsp;coli':&nbsp;50.5,&nbsp;'D.&nbsp;melanogaster':&nbsp;43.<span class="variable-ellipsis">...</span></code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>dict</code></font></td>
<td><b><a href="weblogolib-module.html#std_sizes"><code>std_sizes</code></a></b> = <span title="{'small': LogoSize(
    stack_height=27.0,
    stack_width=5.4000000000000004
), 'large': LogoSize(
    stack_height=81.000000000000014,
    stack_width=16.200000000000003
), 'medium': LogoSize(
    stack_height=54.0,
    stack_width=10.800000000000001
)}"><code>{'small':&nbsp;LogoSize(&nbsp;&nbsp;&nbsp;&nbsp;stack_height=27.0,&nbsp;&nbsp;&nbsp;<span class="variable-ellipsis">...</span></code>
</span></td></tr>
<tr><td align="right" valign="top" width="15%"><font size="-1"><code>dict</code></font></td>
<td><b><a href="weblogolib-module.html#std_units"><code>std_units</code></a></b> = <span title="{'digits': 0.43429448190325176, 'kcal/mol': 0.59242404999999998, 'kJ/mol': 2.4789598268000002, 'probability': None, 'nats': 1.0, 'kT': 1.0, 'bits': 1.4426950408889634}"><code>{'digits':&nbsp;0.43429448190325176,&nbsp;'kcal/mol':&nbsp;<span class="variable-ellipsis">...</span></code>
</span></td></tr>
</table><br />


<!-- =========== START OF FUNCTION DETAILS =========== -->
<table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="details">
  <th colspan="2">Function Details</th></tr>
</table>

<a name="eps_formatter"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">default_formatter</span>(<span class=sig-arg>logodata</span>,
          <span class=sig-arg>format</span>,
          <span class=sig-arg>fout</span>)</span>
  </h3>
<pre class="literalblock">
Generate a logo in Encapsulated Postscript (EPS)
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>

<a name="eps_formatter"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">eps_formatter</span>(<span class=sig-arg>logodata</span>,
          <span class=sig-arg>format</span>,
          <span class=sig-arg>fout</span>)</span>
  </h3>
<pre class="literalblock">
Generate a logo in Encapsulated Postscript (EPS)
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>

<a name="jpeg_formatter"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">jpeg_formatter</span>(<span class=sig-arg>data</span>,
          <span class=sig-arg>format</span>,
          <span class=sig-arg>fout</span>)</span>
  </h3>
<pre class="literalblock">
Generate a logo in JPEG format.
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>

<a name="pdf_formatter"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">pdf_formatter</span>(<span class=sig-arg>data</span>,
          <span class=sig-arg>format</span>,
          <span class=sig-arg>fout</span>)</span>
  </h3>
<pre class="literalblock">
Generate a logo in PDF format.
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>

<a name="png_formatter"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">png_formatter</span>(<span class=sig-arg>data</span>,
          <span class=sig-arg>format</span>,
          <span class=sig-arg>fout</span>)</span>
  </h3>
<pre class="literalblock">
Generate a logo in PNG format.
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>

<a name="png_print_formatter"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">png_print_formatter</span>(<span class=sig-arg>data</span>,
          <span class=sig-arg>format</span>,
          <span class=sig-arg>fout</span>)</span>
  </h3>
<pre class="literalblock">
Generate a logo in PNG format with print quality (600 DPI) resolution.
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>

<a name="txt_formatter"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">txt_formatter</span>(<span class=sig-arg>logodata</span>,
          <span class=sig-arg>format</span>,
          <span class=sig-arg>fout</span>)</span>
  </h3>
<pre class="literalblock">
Create a text representation of the logo data.
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>

<a name="which_alphabet"></a>
<table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td>
  <h3><span class="sig"><span class="sig-name">which_alphabet</span>(<span class=sig-arg>seqs</span>)</span>
  </h3>
<pre class="literalblock">
Returns the most appropriate unambiguous protien, rna or dna alphabet
for a Seq or SeqList.
</pre>
  <dl><dt></dt><dd>
  </dd></dl>
</td></tr></table>
<br />


<!-- =========== START OF VARIABLE DETAILS =========== -->
<table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="details">
  <th colspan="2">Variable Details</th></tr>
</table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="__version__"></a>
<h3>__version__</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>str</code>

      </dd>
<span title="'3.0b12'">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
<span class="variable-quote">'</span>3.0b12<span class="variable-quote">'</span>                                                               </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="classic"></a>
<h3>classic</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>ColorScheme</code>

      </dd>
<span title="&lt;weblogolib.colorscheme.ColorScheme object at 0x138f790&gt;">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
&lt;weblogolib.colorscheme.ColorScheme object at 0x138f790&gt;               </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="default_color_schemes"></a>
<h3>default_color_schemes</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>dict</code>

      </dd>
<span title="{Alphabet( 'ACDEFGHIKLMNPQRSTVWY', zip('acdefghiklmnpqrstvwy', 'ACDEFGHIKLMNPQRSTVWY') ): &lt;weblogolib.colorscheme.ColorScheme object at 0x1356450&gt;, Alphabet( 'ACGU', zip('acgu', 'ACGU') ): &lt;weblogolib.colorscheme.ColorScheme object at 0x13563d0&gt;, Alphabet( 'ACGT', zip('acgt', 'ACGT') ): &lt;weblogolib.colorscheme.ColorScheme object at 0x13563d0&gt;}">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
{Alphabet( 'ACGT', zip('acgt', 'ACGT') ): &lt;weblogolib.colorscheme.Colo<span class="variable-linewrap">\</span>
rScheme object at 0x13563d0&gt;,
 Alphabet( 'ACGU', zip('acgu', 'ACGU') ): &lt;weblogolib.colorscheme.Colo<span class="variable-linewrap">\</span>
rScheme object at 0x13563d0&gt;,
 Alphabet( 'ACDEFGHIKLMNPQRSTVWY', zip('acdefghiklmnpqrstvwy', 'ACDEFG<span class="variable-linewrap">\</span>
HIKLMNPQRSTVWY') ): &lt;weblogolib.colorscheme.ColorScheme object at 0x13<span class="variable-linewrap">\</span>
56450&gt;}                                                                </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="description"></a>
<h3>description</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>str</code>

      </dd>
<span title="'Create sequence logos from biological sequence alignments.'">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
<span class="variable-quote">'</span>Create sequence logos from biological sequence alignments.<span class="variable-quote">'</span>           </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="formatters"></a>
<h3>formatters</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>dict</code>

      </dd>
<span title="{'eps': &lt;function eps_formatter at 0x1391c30&gt;, 'jpeg': &lt;function jpeg_formatter at 0x1391b30&gt;, 'pdf': &lt;function pdf_formatter at 0x13919f0&gt;, 'txt': &lt;function txt_formatter at 0x1391bf0&gt;, 'png_print': &lt;function png_print_formatter at 0x1391bb0&gt;, 'png': &lt;function png_formatter at 0x1391b70&gt;}">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
{'eps': &lt;function eps_formatter at 0x1391c30&gt;,
 'jpeg': &lt;function jpeg_formatter at 0x1391b30&gt;,
 'pdf': &lt;function pdf_formatter at 0x13919f0&gt;,
 'png': &lt;function png_formatter at 0x1391b70&gt;,
 'png_print': &lt;function png_print_formatter at 0x1391bb0&gt;,
 'txt': &lt;function txt_formatter at 0x1391bf0&gt;}                         </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="std_alphabets"></a>
<h3>std_alphabets</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>dict</code>

      </dd>
<span title="{'protein': Alphabet( 'ACDEFGHIKLMNPQRSTVWY', zip('acdefghiklmnpqrstvwy', 'ACDEFGHIKLMNPQRSTVWY') ), 'dna': Alphabet( 'ACGT', zip('acgt', 'ACGT') ), 'rna': Alphabet( 'ACGU', zip('acgu', 'ACGU') )}">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
{'dna': Alphabet( 'ACGT', zip('acgt', 'ACGT') ),
 'protein': Alphabet( 'ACDEFGHIKLMNPQRSTVWY', zip('acdefghiklmnpqrstvw<span class="variable-linewrap">\</span>
y', 'ACDEFGHIKLMNPQRSTVWY') ),
 'rna': Alphabet( 'ACGU', zip('acgu', 'ACGU') )}                       </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="std_percentCG"></a>
<h3>std_percentCG</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>dict</code>

      </dd>
<span title="{'E. coli': 50.5, 'D. melanogaster': 43.0, 'T. thermophilus': 69.400000000000006, 'H. sapiens': 40.0, 'C. elegans': 36.0, 'S. cerevisiae': 38.0, 'M. musculus': 42.0}">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
{'C. elegans': 36.0,
 'D. melanogaster': 43.0,
 'E. coli': 50.5,
 'H. sapiens': 40.0,
 'M. musculus': 42.0,
 'S. cerevisiae': 38.0,
 'T. thermophilus': 69.400000000000006}                                </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="std_sizes"></a>
<h3>std_sizes</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>dict</code>

      </dd>
<span title="{'small': LogoSize(
    stack_height=27.0,
    stack_width=5.4000000000000004
), 'large': LogoSize(
    stack_height=81.000000000000014,
    stack_width=16.200000000000003
), 'medium': LogoSize(
    stack_height=54.0,
    stack_width=10.800000000000001
)}">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
{'large': LogoSize(
    stack_height=81.000000000000014,
    stack_width=16.200000000000003
),
 'medium': LogoSize(
    stack_height=54.0,
    stack_width=10.800000000000001
),
<span class="variable-ellipsis">...</span>                                                                    </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
<table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td>
<a name="std_units"></a>
<h3>std_units</h3>
<dl>
  <dt></dt>
  <dd>
    <dl>
      <dt><b>Type:</b></dt>
      <dd>
          <code>dict</code>

      </dd>
<span title="{'digits': 0.43429448190325176, 'kcal/mol': 0.59242404999999998, 'kJ/mol': 2.4789598268000002, 'probability': None, 'nats': 1.0, 'kT': 1.0, 'bits': 1.4426950408889634}">      <dt><b>Value:</b></dt>
      <dd><table><tr><td>
<pre class="variable">
{'bits': 1.4426950408889634,
 'digits': 0.43429448190325176,
 'kJ/mol': 2.4789598268000002,
 'kT': 1.0,
 'kcal/mol': 0.59242404999999998,
 'nats': 1.0,
 'probability': None}                                                  </pre>
        </td></tr></table></dd>
</span>    </dl>
  </dd>
</dl></td></tr></table>
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